Journal
MOLECULAR SYSTEMS BIOLOGY
Volume 8, Issue -, Pages -Publisher
WILEY
DOI: 10.1038/msb.2012.12
Keywords
combinatorial complexity; mathematical modelling; network mapping; signal transduction; visualisation
Categories
Funding
- JSPS
- SSF (Japan)
- Lions
- Swedish Research Council
- German Ministry for Education and Research (BMBF)
- European Commission [201142, 35995, 043310, 514169]
- MULTIDISCIPLINARY BIO Sweden-Japan initiative (Sweden: Foundation for Strategic Research SSF and Vinnova, Japan: Japan Science and Technology Agency JST)
- Swedish Research Council [2007-4905]
- Grants-in-Aid for Scientific Research [22136001, 22136003] Funding Source: KAKEN
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Intracellular signalling systems are highly complex. This complexity makes handling, analysis and visualisation of available knowledge a major challenge in current signalling research. Here, we present a novel framework for mapping signal-transduction networks that avoids the combinatorial explosion by breaking down the network in reaction and contingency information. It provides two new visualisation methods and automatic export to mathematical models. We use this framework to compile the presently most comprehensive map of the yeast MAP kinase network. Our method improves previous strategies by combining (I) more concise mapping adapted to empirical data, (II) individual referencing for each piece of information, (III) visualisation without simplifications or added uncertainty, (IV) automatic visualisation in multiple formats, (V) automatic export to mathematical models and (VI) compatibility with established formats. The framework is supported by an open source software tool that facilitates integration of the three levels of network analysis: definition, visualisation and mathematical modelling. The framework is species independent and we expect that it will have wider impact in signalling research on any system. Molecular Systems Biology 8: 578; published online 24 April 2012; doi:10.1038/msb.2012.12
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